If I were to upgrade to Lion from my mac pro 1,1 currently running snow leopard) will my flashed card work? I'm Thinking it would change settings or something. Sorry guys I'm not that tech savvy. Thank you

If the flashed card is currently working under snow leopard without any additional kexts installed then the card will function fine under lion. If you installed any additional software/files to snow leopard for the card to work (Which I dont believe you need to) make sure you have another oem gpu to do the upgrade to lion and then install those kexts.